eProtein Database is the part of ePath3D which contains the proteins that are associated with the
ePathway Database. One can also enter their own protein data into this database and link with pathways. Both, the eProtein Database and the ePathway Database are part of the ePath3D software, there are no additional charges for these database.

Edit: To edit References,
of currently selected protein click
“Modify References” Button,
and then make changes as required.
You can change Authors’ name,
Journal’s Name, Title and Pubmed
Id. Click “Save References”
to save the changes.

Add: To add References,
of currently selected protein click
“Modify References” Button,
and click on the blank row with asterisk
mark (*). Fill in the following information
in respective boxes, i.e., Authors’
Name, Journal’s Name, Title
and Pubmed id. Click “Save References”
button to save the changes.

Delete: To delete
References, of currently selected
protein click “Modify References”
Button, and click on the row header
(blank space showing the arrow mark
to indicate currently selected Reference),
and then press Keyboard delete button.
To save the changes, click on “Save
References” button.

Edit: To edit References,
of currently selected protein click
“Modify References” Button,
and then make changes as required.
You can change Authors’ name,
Journal’s Name, Title and Pubmed
Id. Click “Save References”
to save the changes.

Add: To add References,
of currently selected protein click
“Modify References” Button,
and click on the blank row with asterisk
mark (*). Fill in the following information
in respective boxes viz. Authors’
Name, Journal’s Name, Title
and Pubmed id. Click “Save References”
button to save the changes.

Delete: To delete
References, of currently selected
protein click “Modify References”
Button, and click on the row header
(blank space showing the arrow mark
to indicate currently selected Reference),
and then press Keyboard delete button.
To save the changes, click on “Save
References” button.

The pathways folder lists
the pathways which are related to
the selected protein. Click on the
Pathway Title, to view 3D Pathway
Image with its detail description
and References. To Open Pre-made pathway
on ePath3D, click on the Pathway Image.

Edit: To edit References,
of currently selected protein click
“Modify References” Button,
and then make changes as required.
You can change Authors’ name,
Journal’s Name, Title and Pubmed
Id. Click “Save References”
to save the changes.

Add: To add References,
of currently selected protein click
“Modify References” Button,
and click on the blank row with asterisk
mark (*). Fill in the following information
in respective boxes viz. Authors’
Name, Journal’s Name, Title
and Pubmed id. Click “Save References”
button to save the changes.

Delete: To delete
References, of currently selected
protein click “Modify References”
Button, and click on the row header
(blank space showing the arrow mark
to indicate currently selected Reference),
and then press Keyboard delete button.
To save the changes, click on “Save
References” button.

The publications folder list
the publications which are related
to the selected protein. The publications
are retrieved from the NCBI PubMed.

*Publication
extracted from NCBI (The National
Center for Biotechnology Information),
Pubmed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed)TOP

siRNA
Database

The siRNA database contains
siRNA targets against the selected
protein's mRNA sequence.The program
output is ranked by the degree of
specificity of the predicted siRNAs.

Parameters:

The parameters for the siRNA Database
are based on the methods developed
for siRNA prediction by Dr. Thomas
Tuschl (Max-Planck Institut).

BEST TARGET: The
'Best Target' for siRNA is nearest
to the mRNA start sequence. Those
siRNA targets which are nearest to
the start sequence produce a better
'Knock-Down' due to cleavage of a
great segment of the mRNA.

All siRNA targets have been screened
to remove any siRNA which shares homology
with other sequences, thus producing
targets which are specific to the
gene of interest.

Target Selection Method:

Target Size: 19-22 Nucleotides

Nucleotide target from 5' and 3':
50 (Optimum). The search for target
start after 50 nucleotide for sequences
size more than 200. Ignored for sizes
less than 200 nucleotide.

Nucleotide Target For siRNA:
Either "AA" (Optimum) or
"T"

G+C Content: 47-51%
Optimum (10-90% are also taken in
account if optimum fails)

'A' Repeats: <
4 (i.e motif will have less then or
equal to 4 A's repeats)

'T' Repeats: <
4 (i.e motif will have less then or
equal to 4 T's repeats)

'G' Repeats: <
3 (i.e motif will have less then or
equal to 3 G's repeats)

'C' Repeats: <
3 (i.e motif will have less then or
equal to 3 C's repeats)

This database contains antigenic
peptide targets against the protein
sequence of the selected protein.
The most important aspect in the production
of antibodies or drug is the design
of the peptide-antigen. The peptide-antigen
is a small segment (15-18 amino acids)
of the protein sequence of interest.
These peptide-antigens can be used
for immunization in order to produce
antibodies against the protein for
which the peptide is from or the peptides
can be used as a basis for small-molecule/drug
targeting. All peptide targets are
linked to Protein Lounge's proprietary
hyrdoplotting tool, which allows you
to view an interactive version of
the protein sequence on a hydrophilicity/phobicity
plot.

Parameters:

The parameters of the Peptide-Antigen
Database are based on the methods
for peptide selection developed by
Dr. Philip Goulder (Oxford), Dr. Otto
Yang (UCLA) and Dr. Andrew Bradbury
(LANL).

BEST TARGET: The
'Best Target' is the peptide which
is the most hydrophilic, thus it is
the region of the protein which has
the best chance of surface exposure.

The Kinase and Phosphatase
database is a list of all protein
kinases and protein phosphatases.
This database is of particular importance
for drug discovery. It is very important
to understand the proteins which phosphorylate
(kinases) and those which dephosphorylate
(phosphatases) signaling proteins.
The Protein Lounge Kinase/Phosphatase
listing is the only currently available
list of both kinases and phosphatases.TOP

Transcription
Factor Database

The Protein Lounge Transcription
Factor Database is a resource housing
information relating to transcription
factors of humans and other organisms.
This database is organized by the
transcription factor names, organism
specification, binding sequences,
binding elements and cell type specification.

Transcription factors are proteins
involved in the regulation of gene
expression that bind to the promoter
elements upstream of genes and either
facilitate or inhibit transcription.
Through this process they control
and regulate gene expression. Transcription
factors are composed of two essential
functional regions: a DNA-binding
domain and an activator domain. The
DNA-binding domain consists of amino
acids that recognize specific DNA
bases near the start of transcription.

The Transcription Factor database
contains all necessary information
about the transcription factors such
as its classification, specific functions,
DNA sequence, domains, structures,
interaction with other proteins, its
allied members and role in specific
diseases. One can also get information
about the pathways related to the
specific transcription factors. It
is our goal to offer a reliable up-to-date
resource on transcription factors
that can be utilized by researchers
in studying gene expression.TOP

The parameters for the siRNA
Database are based on the methods
developed for siRNA prediction by
Dr. Thomas Tuschl (Max-Planck Institute).

Functionality:

Enter DNA Sequence:

It contains the DNA sequence of selected
Protein. The Sequence is editable
and replaceable.

Parameters:

Region to Search
for siRNA indicates the Coding
Region of the Sequence to search for
siRNA's. It can be changed by the
user to select any portion from the
sequence. This is the region of interest
to search for siRNA's. The siRNA search
will start from within this region
taking into account other search values.

Nucleotide target
from 5' and 3 value indicates
that the search for siRNA fragments
will not account for the number of
nucleotide mention in this text box
from the start of the DNA sequence
& end of the Dna sequence between
the Region to search for siRNA nucleotide.
This option is neglected for sequences
which are smaller than 200 bp.

siRNA Size
is the length of siRNAs, program would
attempt to generate.

First Nucleotide
target of siRNA is the nucleotide
for which the program would attempt
to search with in the given nucleotide
sequence. The program would search
for nucleotide target after the 51(Region
to Search for siRNA + Nucleotide target
from 5' and 3'. Default is 'AA'.

G+C Content
boxes displays the % of G's and C's
the siRNA fragments should have.

The Avoid 'A'
repeats, Avoid 'T' repeats, Avoid
'C' repeats, Avoid 'G' repeats
displays the values which will be
avoided while search. This implies
that the siRNA fragments displayed
will not have consecutive repeats
of A's, T's, G's, C's for the values
given.

Generate siRNA:

When clicked on this button, program
would start searching for the siRNA
in the given DNA sequence. It would
display the results just below.

The parameters of the Peptide-Antigen
Database are based on the methods
for peptide selection developed by
Dr. Philip Goulder (Oxford), Dr. Otto
Yang (UCLA) and Dr. Andrew Bradbury
(LANL). The tool will find the regions
on the entered protein sequence which
are most antigenic, thus will make
good drug or antibody targets.

Parameters:Peptide Length
is the length of peptide, program
would attempt to generate. Default
is 15 AAs. It can be change as per
requirement.

Peptide Overlap
By determines, how many AAs will be
included while generating the next
peptide. Default is 10 AAs.

krhgpgpreargar
gpreargarpglrv

Shorten By
determines how much the program will
shorten the peptide, in case it find
N-Forbidden AAs or C-Forbidden AAs.
Here, the default is 3. That's why
peptide length may vary between 12
and 17, if Lengthen By is 2 and Shorten
By is 3 and Peptide

Lengthen By
determine how much the program will
lengthen the peptide, if it find 15
down to 12 are forbidden (in default
case).

C-Term Forbidden
AAs restrict peptides which
ends with these AAs. If program find
C-Forbidden peptides at the end of
peptide it'll shorten or lengthen
the peptide to find Non-Forbidden
peptide. Default is GPEDQNTSC.

N-Term Forbidden
AAs restrict peptides which
start with these AAs. Default is 'Q'.

Generate Peptide:

When click on this button, it will
start searching for best possible
peptides using given parameters. The
Program will automatically discard
any Peptides with less then -1 hydrophilicty.
The results of this are presented
in the below screen shot.

Hydroplot:

It'll display a pop-window with Kyte-Dolittle
Graph aligned with the peptide and
protein sequences. You can highlight
the plot to view the corresponding
region on protein sequence.

Changing Organism
Database: Select the organism
from drop-down list, to view the protein
database of that Organism.

Changing Database
Type: To Change the currently
selected database to any other database(i.e.
Kinase, Phosphatase, Pathway Proteins,
Transcription Factor and All Proteins),
select it from drop-down list.

View By Pathways:
Select any Pathway from drop-down
list, it would show the list of proteins
related to the selected Pathway.

View By Category:
Select any Protein Category from drop-down
list, to view the list of protein
exist in that Category.

To Search protein, specify
the protein name or gen bank no or
Full Name in "Enter Search Term"
box. And then click "Go"
Button to search for specified protein.
The results will me displayed in Protein
Data Grid.

Edit: To
edit Protein data, click on “Modify
Protein” Button, and then make
changes as required. You can modify
Protein name, Gen Bank No. and Full
Name of Protein but cannot edit Organism.
Click “Save Protein” to
save the changes.

Add: To add Protein,
click on “Add Protein”
Button, and click on the blank row
with asterisk mark (*); it is always
the last record. Fill in the following
information in respective boxes viz.Protein’
Name, Gen Bank No., and Full Name.
Click “Save Protein” button
to save the changes.

Delete: To delete
protein click on “Modify Protein”
Button, then select the protein you
want to delete, and then press Keyboard
delete button. To save the changes,
click on “Save Protein”
button.